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CrystFEL - Data processing for serial crystallography
-----------------------------------------------------
Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
a research centre of the Helmholtz Association.
Authors:
Thomas White <taw@physics.org>
Richard Kirian <rkirian@asu.edu>
Kenneth Beyerlein <kenneth.beyerlein@desy.de>
Andrew Aquila <andrew.aquila@cfel.de>
Andrew Martin <andrew.martin@desy.de>
Lorenzo Galli <lorenzo.galli@desy.de>
Chun Hong Yoon <chun.hong.yoon@desy.de>
Kenneth Beyerlein <kenneth.beyerlein@desy.de>
Karol Nass <karol.nass@desy.de>
Nadia Zatsepin <nadia.zatsepin@asu.edu>
Anton Barty <anton.barty@desy.de>
Cornelius Gati <cornelius.gati@desy.de>
Fedor Chervinskii <fedor.chervinskii@gmail.com>
Alexandra Tolstikova <alexandra.tolstikova@desy.de>
Wolfgang Brehm <wolfgang.brehm@gmail.com>
Valerio Mariani <valerio.mariani@desy.de>
Parker de Waal <Parker.deWaal@vai.org>
Takanori Nakane <nakane.t@gmail.com>
Keitaro Yamashita <k.yamashita@spring8.or.jp>
Mamoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp>
Thomas Grant <tgrant@hwi.buffalo.edu>
Steve Aplin <steve.aplin@desy.de>
Oleksandr Yefanov <oleksandr.yefanov@desy.de>
Helen Ginn <helen@strubi.ox.ac.uk>
Nicolas Riebesel <nicolas.riebesel@tuhh.de>
Yaroslav Gevorkov <yaroslav.gevorkov@desy.de>
Omri Mor <omor1@asu.edu>
--------------------------------------------------------------------------------
CrystFEL is free software: you can redistribute it and/or modify it under the
terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
CrystFEL. If not, see <http://www.gnu.org/licenses/>.
--------------------------------------------------------------------------------
CrystFEL is a suite of programs for processing (and simulating) Bragg
diffraction data from "serial crystallography" experiments, often (but not
always) performed using an X-ray Free-Electron Laser. Some of the particular
characteristics of such data which call for a specialised software suite are:
- The sliced, rather than integrated, measurement of intensity data. Many, if
not all reflections are partially integrated.
- Many patterns (thousands) are required - high throughput is needed.
- The crystal orientations in each pattern are random and uncorrelated, meaning
that:
- Merging into lower symmetry point groups may require the resolution of
indexing ambiguities.
CrystFEL includes programs for simulating and processing patterns subject to the
above characteristics. The main data processing pipeline is defined by four
programs:
- indexamajig, for bulk indexing and integration of diffraction patterns
- process_hkl, for quickly merging per-pattern lists of intensities into
a single reflection list
- partialator, for merging patterns more accurately (and much more
slowly) using scaling, partiality modelling and
post refinement
- ambigator, for resolving indexing ambiguities
There are two tools for calculating figures of merit for reflection data:
- compare_hkl, for figures of merit that involve comparing two sets of
data, like CC* and R_split
- check_hkl, for figures of merit based on only one set of data, like
completeness, redundancy and twinning tests
Three tools are provided for visualising data:
- cell_explorer, for examining distributions of lattice parameters
- hdfsee, an image viewer
- render_hkl, for turning reflection lists into pretty graphics
CrystFEL can also simulate data, e.g. for methods development:
- pattern_sim, which performs a Fourier image calculation
- partial_sim, which calculates reflection intensities based on a
partiality calculation and optionally plots the peaks
in an image
There are also five utility programs:
- get_hkl, for doing various simple operations on reflection lists such
as expanding by symmetry or adding noise
- cell_tool, for doing operations on unit cells such as applying
transformations or looking for indexing ambiguities
- geoptimiser, for refining detector geometry.
- list_events, for creating event lists from multi-event files.
- make_pixelmap, for creating HDF5 pixel map files for other programs
like Cheetah and OnDA
- whirligig, for finding multiple shots from single crystals.
There is also a folder full of scripts for achieving many related tasks, such as
file format conversion.
Standard "man" pages are provided for documentation, or you can invoke any
program with the argument "--help" to get a summary of options. There are some
example geometry and beam description files in doc/examples, and API
documentation created using Doxygen.
Installation
------------
The terse installation instructions below should be enough if you're experienced
with installing software from source. More detailed installation information is
available on the website:
https://www.desy.de/~twhite/crystfel/install.html
Mandatory dependencies:
- CMake 3.12 or later
- HDF5 1.8.0 or later (1.10.0 or later preferred)
- GNU Scientific Library (GSL)
- Bison 2.6 or later
- Flex
- Zlib (1.2.3.5 or later preferred)
"Optional" dependencies:
- GTK2 or later (GTK3 preferred)
- Cairo
- Pango
- gdk-pixbuf
- NCurses
- libPNG
- libTIFF
- FFTW3
- XGandalf (https://stash.desy.de/users/gevorkov/repos/xgandalf)
"Optional" run-time dependencies:
- Mosflm (https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/)
- DirAx (http://www.crystal.chem.uu.nl/distr/dirax/)
- XDS (http://xds.mpimf-heidelberg.mpg.de/)
Note that "optional" means that you *can* install CrystFEL without them, however
your installation will lack important components such as the visualisation
tools and certain indexing algorithms.
For processing electron diffraction or wide-bandwidth X-ray data, you should
also install PinkIndexer from:
https://stash.desy.de/users/gevorkov/repos/pinkindexer
Installation follows the normal CMake procedure:
$ mkdir build
$ cd build
$ cmake ..
$ make
$ sudo make install
If external libraries have been installed in non-standard locations, you can set
the path like this, for example for Xgandalf:
cmake -DXGANDALF_INCLUDES=/path/to/xgandalf/include \
-DXGANDALF_LIBRARIES=/path/to/xgandalf/lib/libxgandalf.so
The path to HDF5 can be set similarly:
cmake -DHDF5_ROOT=/path/to/hdf5 (... /include, /lib etc)
To install CrystFEL in a custom location, use:
cmake -DCMAKE_INSTALL_PREFIX=/path/for/crystfel/installation
Funding acknowledgements
------------------------
Development of CrystFEL is primarily funded by the Helmholtz Association.
Partial funding for CrystFEL has previously been provided by:
- "X-Probe", a project of the European Union's 2020 Research and Innovation
Program Under the Marie Skłodowska-Curie grant agreement 637295 (2015-2018).
- The BMBF German-Russian Cooperation "SyncFELMed", grant 05K14CHA (2014-2017).
- BioStruct-X, a project funded by the Seventh Framework Programme (FP7) of the
European Commission (2011-2016).
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